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an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.

(X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.

a tool that utilizes deep learning to perform volumetric electron microscopy image segmentations, both semantic and instance segmentation.

is a tool designed to expand structure prediction sampling by optimizing the parallelization of AlphaFold-based predictions across GPU clusters. It automatically splits large prediction runs into batches distributed across multiple GPUs, with alignment computations performed on CPUs, and gathers all results into a single ranked output with comprehensive visualization plots. The tool supports AFmassive, ColabFold, and AlphaFold3 as inference engines and is optimized for SLURM workload managers, while remaining usable for sequential execution on single-GPU servers.

is a diffusion framework designed for generating 3D drug-like molecules, achieving a sampling success rate of over 99%. This tool addresses the atom-bond inconsistency problem in 3D molecule diffusion generation and serves as a backbone for applications such as pocket-based generation and linker generation.

is GPU-Accelerated Python STOPgap for Template Matching for fast template matching (TM) in cryo electron tomograms that is based on TM routines from STOPGAP.

is a tool for conditioning diffusion models to generate 3D drug-like molecules, built on the MolDiff codebase. It integrates pretrained models and provides a streamlined workflow for sampling molecules from defined pockets, making it suitable for structure-based drug design applications. The software supports various data processing tasks, including dataset preparation and evaluation of generated molecules.

is a Python package to search/retrieve/filter proteins and protein structures.

(Crystallographic Object-Oriented Toolkit) an application that supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.

(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.